FI:PB050 Modelling in Bioinformatics - Course Information
PB050 Modelling and Prediction in Systems BiologyFaculty of Informatics
- Extent and Intensity
- 1/1. 2 credit(s) (plus extra credits for completion). Type of Completion: zk (examination).
- doc. RNDr. David Šafránek, Ph.D. (lecturer)
- Guaranteed by
- prof. Ing. Václav Přenosil, CSc.
Department of Machine Learning and Data Processing - Faculty of Informatics
- Thu 18:00–19:50 B411
- This is an interdisciplinary course that extends the knowledge of bachelor students of all study branches. The course is especially recommended for students of Bioinformatics.
- Course Enrolment Limitations
- The course is also offered to the students of the fields other than those the course is directly associated with.
- fields of study / plans the course is directly associated with
- Applied Informatics (programme FI, B-AP)
- Bioinformatics (programme FI, B-AP)
- Economic Information Systems (programme ESF, B-SI)
- Informatics with another discipline (programme FI, B-BI)
- Informatics with another discipline (programme FI, B-FY)
- Informatics with another discipline (programme FI, B-GE)
- Informatics with another discipline (programme FI, B-GK)
- Informatics with another discipline (programme FI, B-CH)
- Informatics with another discipline (programme FI, B-IO)
- Informatics with another discipline (programme FI, B-MA)
- Informatics with another discipline (programme FI, B-TV)
- Informatics (programme FI, B-IN)
- Public Administration Informatics (programme FI, B-AP)
- Mathematical Informatics (programme FI, B-IN)
- Mathematics with Informatics (programme PřF, N-MA)
- Parallel and Distributed Systems (programme FI, B-IN)
- Computer Graphics and Image Processing (programme FI, B-IN)
- Computer Networks and Communication (programme FI, B-IN)
- Computer Systems and Data Processing (programme FI, B-IN)
- Programmable Technical Structures (programme FI, B-IN)
- Embedded Systems (programme FI, N-IN)
- Service Science, Management and Engineering (programme FI, N-AP)
- Social Informatics (programme FI, B-AP)
- Artificial Intelligence and Natural Language Processing (programme FI, B-IN)
- Course objectives
- At the end of the course, students will be able to:
understand complex models of biological processes;
apply abstract computer-scientific thinking to modeling and analysis of complex systems with special focus to biological systems;
practically use free modeling and analysis software tools;
perform static analysis of large-scale interaction networks;
model and analyze dynamic properties of interaction networks
- History and scope of systems biology.
- Basic notions: living organism as a system with precisely given structure and functionality, in silico model, abstraction, simulation and prediction, model validation.
- Sources of biological data: databases of biological knowledge, databases of biological models.
- Specification of a biological model: biological networks and pathways, languages SBML and SBGN.
- Static analysis of biological systems: analysis of biological networks and pathways, network motifs and biological circuits.
- Modeling and simulation of biological systems dynamics: hypotheses prediction.
- Modeling of Escherichia coli bacteria: genetic regulatory network, models of loccomotion organ synthesis and chemotaxis, nutritional stress response models.
- Model parameters, robustness and parameter sensitivity.
- recommended literature
- ALON, Uri. An Introduction to Systems Biology: Design Principles of Biological Circuits. : Chapman & Hall/Crc, 2006. info
- not specified
- VRIES, Gerda de. A course in mathematical biology : quantitative modeling with mathematical and computational methods. Philadelphia, Pa.: Society for Industrial and Applied Mathematics, 2006. xii, 309. ISBN 0898716128. info
- NOBLE, Denis. Music of life : biology beyond the genome. Oxford: Oxford University Press, 2006. xiii, 153. ISBN 9780199295739. info
- System modeling in cell biology : from concepts to nuts and bolts. Edited by Zoltan Szallasi - Jorg Stelling - Vipul Periwal. Cambridge, Mass.: MIT Press, 2006. xiv, 448. ISBN 0262195488. info
- Computational modeling of genetic and biochemical networks. Edited by James M. Bower - Hamid Bolouri. Cambridge: Bradford Book, 2001. xx, 336. ISBN 0262524236. info
- Teaching methods
- Lectures and optional homeworks. Group projects.
- Assessment methods
- Written final examination (50%), semester project (50%).
- Language of instruction
- Follow-Up Courses
- Further Comments
- Study Materials
The course is taught annually.